SIV infection and ARV treatment reshape the transcriptional and epigenetic profile of naïve and memory T cells in vivo (ATAC-Seq)

Here we use RNAseq and ATACseq to study the transcriptomics and epigenetic landscape of longitudinally sampled naïve and memory CD4+ and CD8+ T cells in two species of non-human primates prior to SIV infection, during chronic SIV infection, and after administration of ARVs. We find that SIV infection leads to significant alteration to the transcriptomic profile of all T cell subsets that are only partially reversed by administration of ARVs. Epigenetic changes were more apparent in animals with longer periods of untreated SIV infection and correlated well with changes in corresponding gene expression. Known SIV integration sites did not vary due to SIV status but did contain more open chromatin in rhesus macaque memory T cells, and the expression of proteasome-related genes at the pre-SIV timepoint correlated with subsequent viremia. RNAseq and ATACseq of longitudinally sampled naïve and memory CD4+ and CD8+ T cells in rhesus macaques and pig-tail macaques prior to SIV infection, during chronic SIV infection, and after administration of ARVs.